Introduction

Some Informations about the projekt here would be really nice.

Analysis

2.1a Fraction of Xenelogs vs. Number of Genes

Q: Is there a dependence on the size of the gene tree, i.e., the number of species and genes? ?

Short description of the task at hand.

Tab. 1: Dependecy of the size of the gene tree in respect to th number of species. Results of for each Group, slope und intercept of a linear model were calculated as well as the spearman correlation value.
Group Duplication_Rate Loss_Rate HGT_Rate Slope Intercept Spearman_Corr
P0 0.25 0.25 0.25 0.0014 0.23 0.21
P1 0.50 0.50 0.50 -0.0009 0.39 0.05
P2 0.50 0.50 1.00 -0.0012 0.48 -0.02
P3 0.50 0.50 1.50 -0.0021 0.58 -0.16
P4 1.00 1.00 0.50 -0.0011 0.40 0.04
P5 1.00 1.00 1.00 -0.0016 0.53 -0.14
P6 1.50 1.50 1.50 -0.0016 0.57 -0.24

2.1a Plots: Fraction of Xenelogs vs. Number of Genes

Each plot needs a short discription. This can be done here. Maybe it is better not to iterate over the goups. maybe we should split the following coe into \(7\) seperate sektions, so we can write a custom text for each. But I guess an overall discription is fine as well... less work ;)

Some text here. . .

2.1a Fraction of Xenologs vs. Number of Species

Each plot needs a short discription. This can be done here. Maybe it is better not to iterate over the groups. Maybe we should split the following code into \(7\) seperate sektions, so we can write a custom text for each.

Tab. 2: Dependecy of the size of the gene tree in respect to th number of species. Results of for each Group, slope und intercept of a linear model were calculated as well as the spearman correlation value.
Group Duplication_Rate Loss_Rate HGT_Rate Slope Intercept Spearman_Corr
P0 0.25 0.25 0.25 0.0015 0.23 0.09
P1 0.50 0.50 0.50 0.0004 0.34 0.04
P2 0.50 0.50 1.00 0.0004 0.42 0.02
P3 0.50 0.50 1.50 -0.0022 0.55 -0.09
P4 1.00 1.00 0.50 0.0002 0.34 0.02
P5 1.00 1.00 1.00 -0.0016 0.49 -0.04
P6 1.50 1.50 1.50 0.0001 0.46 0.00

2.1a Plots: Fraction of Xenelogs vs. Number of Species

Each plot needs a short discription. This can be done here. Maybe it is better not to iterate over the groups. Maybe we should split the following code into \(7\) seperate sections, so we can write a custom text for each. But I guess an overall discription is fine as well... less work ;)

Some text here. . .

2.1b Fraction of Xenelogs with fixed HGT

How does the fraction depend on the rate of duplications and losses for a fixed horizontal transfer rate?

Some text was was done here. And maybe why?

Plot: Duplication Rate

Short introduction

Boxplot of the Fraction of Xenologs plotted against the duplication rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

Boxplot of the Fraction of Xenologs plotted against the duplication rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

In XX we see examples of plotting in R. Explanation of the graph

Plot: Loss Rate

Short introduction

Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

In XX we see examples of plotting in R. Explanation of the graph

2.1c

How does the fraction depend on the horizontal transfer rate on the the rate of duplications and losses?

How does the fraction depend on the horizontal transfer rate with a fixed duplication and loss rate? --> fixed Question??

2.1c Plots Fraction vs. HGT fixes Loss

DIE PLOTS SIND NICHT ZUFRIEDENSTELLEND. PAUL HAST DU EINE TOLLE IDEE WIE WIR DAS GUT DARSTELLEN KÖNNEN

Ab Zeile \(205-258\) im tree_analyze.RScript falls da jmd rumexperimentieren mag. Überschrift "To-Do"

Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

2.1c Plots Fraction vs. HGT fixed Duplikation

DIE PLOTS SIND NICHT ZUFRIEDENSTELLEND. PAUL HAST DU EINE TOLLE IDEE WIE WIR DAS GUT DARSTELLEN KÖNNEN

Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

Boxplot of the Fraction of Xenologs plotted against the loss rate with a fixed horizontal gene transfer (HGT) rate. The different colors marking the groups with the same HGT rate.

2.1d

How does the fraction depend on the frequency of multifurctions.

2.1d Plot

AUCH HIER GEFÄLLT MIR DER PLOTT ÜBERHAUPT NICHT. BOXPLOT ÜBER ALLE GRUPPEN? ODER 6 EINZELNE PLOTS FÜR JEDE GRUPPE MIT LINEAREM ODER x^2 MODEL? ODER WIR BILDEN "BUCKETS" MIT x=NON_BINARY_PROB VS y=FRACTION_OF_XENOLOGS. und wir bilden buckets mit 1 = [0-0.1], 2 = [0.1-0.2], 3 = [0.2-0.3] usw..

caption = "Wasn hier zu sehen??"

plot(x = treeDataDf$non_binary_prob,
     y = treeDataDf$Fraction_of_Xenologs)
Wasn hier zu sehen??

Wasn hier zu sehen??

2.2 Fitch from LDT with CD

Second we consider the dependencies for the edges in Fitch graphs computed from an LDT graph. Here the following variants should be considered:

  • Complete multipartite graph obtained by solving the Cluster Deletion Problem for the complement of the LDT (see webpage).
  • The \(rs-Fitch\) graph of the scenario computed with “Algorithm 1” from Rbelow.pdf (the latter is already implemented in AsymmeTree).@

@Paul, hast du hier nicht schonmal was angefangen?

In meinem Script finde ich dazu nichts.

Plots

Die können hier eingefügt werden

3. Triples: Characterization of LDT Graph

The triple set \(T (G)\) is related to the gene tree, while the triple set \(S(G, σ)\) is related to the species tree. It is therefore of interest to compare to what extent \(T (G)\) and \(S(G, σ)\) overlap the triple sets of true gene tree and the triple set of the true species tree, respectively. How can this be quantified in a meaningful way? Again we are interested in the dependence of the simulation parameters.

Tab. 3: Some Caption
Group recall_cd_mean_100 recall_cd_mean_80 recall_cd_mean_60 recall_cd_mean_40 recall_cd_mean_20
P0 0.67 0.66 0.65 0.61 0.50
P1 0.67 0.66 0.64 0.59 0.51
P2 0.67 0.66 0.66 0.63 0.56
P3 0.70 0.70 0.68 0.65 0.58
P4 0.64 0.63 0.63 0.58 0.49
P5 0.69 0.69 0.68 0.65 0.56
P6 0.69 0.68 0.67 0.64 0.61
Tab. 4: Some Caption
Group precision_cd_mean_100 precision_cd_mean_80 precision_cd_mean_60 precision_cd_mean_40 precision_cd_mean_20
P0 0.85 0.86 0.89 0.88 0.87
P1 0.88 0.88 0.91 0.91 0.90
P2 0.91 0.92 0.93 0.93 0.94
P3 0.94 0.95 0.95 0.96 0.96
P4 0.86 0.87 0.88 0.88 0.89
P5 0.93 0.93 0.94 0.94 0.93
P6 0.95 0.95 0.95 0.95 0.97
Tab. 5: Some Caption
Group accuracy_cd_mean_100 accuracy_cd_mean_80 accuracy_cd_mean_60 accuracy_cd_mean_40 accuracy_cd_mean_20
P0 0.97 0.98 0.98 0.99 1.00
P1 0.95 0.96 0.98 0.99 1.00
P2 0.93 0.95 0.97 0.98 1.00
P3 0.92 0.94 0.96 0.98 0.99
P4 0.94 0.96 0.97 0.99 1.00
P5 0.93 0.95 0.97 0.98 1.00
P6 0.92 0.94 0.96 0.98 0.99
Tab. 6: Some Caption
Group recall_rs_mean_100 recall_rs_mean_80 recall_rs_mean_60 recall_rs_mean_40 recall_rs_mean_20
P0 0.70 0.67 0.65 0.62 0.51
P1 0.71 0.69 0.65 0.59 0.53
P2 0.73 0.70 0.69 0.66 0.58
P3 0.75 0.74 0.72 0.67 0.60
P4 0.70 0.66 0.66 0.60 0.52
P5 0.74 0.73 0.71 0.67 0.58
P6 0.75 0.74 0.72 0.68 0.64
Tab. 6: Some Caption
Group precision_rs_mean_100 precision_rs_mean_80 precision_rs_mean_60 precision_rs_mean_40 precision_rs_mean_20
P0 0.83 0.83 0.84 0.86 0.85
P1 0.85 0.85 0.86 0.88 0.89
P2 0.91 0.89 0.91 0.91 0.93
P3 0.92 0.93 0.93 0.94 0.95
P4 0.86 0.84 0.86 0.84 0.90
P5 0.91 0.91 0.91 0.92 0.92
P6 0.94 0.93 0.94 0.94 0.95
Tab. 6: Some Caption
Group accuracy_rs_mean_100 accuracy_rs_mean_80 accuracy_rs_mean_60 accuracy_rs_mean_40 accuracy_rs_mean_20
P0 0.97 0.97 0.98 0.99 1.00
P1 0.95 0.96 0.97 0.99 1.00
P2 0.94 0.95 0.97 0.98 1.00
P3 0.93 0.95 0.97 0.98 0.99
P4 0.95 0.96 0.97 0.99 1.00
P5 0.94 0.95 0.97 0.98 1.00
P6 0.93 0.95 0.96 0.98 0.99

Plots CD

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Plots Fitch (RS)

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle beschreibung des Plottes hier

Sinvolle Beschreibung des Plottes hier

Sinvolle Beschreibung des Plottes hier

Tripple T Plots

Hier stimmt was mit den Daten nicht so ganz. Über all \(1\) drin.

Recall

Beschreibender Text hier.

Beschreibender Text hier.

Summary Table Recall

Tab. 6: Recall
Group T_LDT_Recall_Mean T_LDT_Recall_Median S_LDT_Recall_Mean S_LDT_Recall_Median
P0 1 1 1 1
P1 1 1 1 1
P2 1 1 1 1
P3 1 1 1 1
P4 1 1 1 1
P5 1 1 1 1
P6 1 1 1 1

Precision

Beschreibender Text hier.

Beschreibender Text hier.

Precision Summary

Tab. 6: Precision
Group T_LDT_Precision_Mean T_LDT_Precision_Median S_LDT_Precision_Mean S_LDT_Precision_Median
P0 0.05 0.01 0.07 0.00
P1 0.09 0.04 0.10 0.04
P2 0.13 0.09 0.18 0.11
P3 0.14 0.10 0.23 0.18
P4 0.09 0.04 0.10 0.04
P5 0.12 0.08 0.17 0.11
P6 0.14 0.10 0.20 0.13

Accuracy Plot

Accuracy Beschreibender Text hier.

Accuracy Beschreibender Text hier.

Accuracy Summary

Tab. 6: Precision
Group T_LDT_Precision_Mean T_LDT_Precision_Median S_LDT_Precision_Mean S_LDT_Precision_Median
P0 0.05 0.01 0.07 0.00
P1 0.09 0.04 0.10 0.04
P2 0.13 0.09 0.18 0.11
P3 0.14 0.10 0.23 0.18
P4 0.09 0.04 0.10 0.04
P5 0.12 0.08 0.17 0.11
P6 0.14 0.10 0.20 0.13

Tripple S

Recall

Recall: Beschreibender Text hier.

Recall: Beschreibender Text hier.

Precision

Precision: Beschreibender Text hier.

Precision: Beschreibender Text hier.

Accuracy

Accuracy: Beschreibender Text hier.

Accuracy: Beschreibender Text hier.

Tripple T Fraction

Tripple T Fraction: Beschreibender Text hier.

Tripple T Fraction: Beschreibender Text hier.

Tripple S Fraction

Tripple S Fraction: Beschreibender Text hier.

Tripple S Fraction: Beschreibender Text hier.